I have some questions regarding the FsFastIndividual pipeline. I hope you can take a look at the commands I have run and give me some insight into what the problem might potentially be. I have 5 rotating wedge stimuli runs

1. I set up my subject's directories according to the freesurfer tutorial powerpoint and declare my environmental variables using-

<export FREESURFER_HOME=/Volumes/RCBI/freesurfer

export SUBJECTS_DIR=/Volumes/rcbiUsers/dcole/Retinotopy

source $FREESURFER_HOME/SetUpFreeSurfer.sh>

Bold data renamed to f.nii.gz and placed into run folders (001, 002, etc)

2. I then reconstruct the strucutural data using-

<recon-all -i /Volumes/rcbiUsers/dcole/Retinotopy/VG01/raw/VGP01_001.dcm -subjid VG01>

3. I create the subjectname file, run preprocessing, and make the analysis files.

<preproc-sess -surface self lhrh -fwhm 5 -sf sessid -fsd bold

mkanalysis-sess -analysis rtopy.self.lh -surface self lh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5

mkanalysis-sess -analysis rtopy.self.rh -surface self rh -TR 1.2 -abblocked 38.4 -fsd bold -fwhm 5>

4. Then I run the analysis using-

<selxavg3-sess -analysis rtopy.self.lh -sf sessid

selxavg3-sess -analysis rtopy.self.lh -sf sessid>

~This step was giving me an error until I added "faux" eccentricity run folders with runs 1-5 functional data copied and rtopy.par files with stimtype eccen. Rerunning these 2 steps with the faux eccentricity data fixed the error message.

5. Create occipital patch with (http://www.alivelearn.net/?p=65) as guideline. Flatten patch using-

<mris_flatten -w 0 -distances 20 7 lh.occip.patch.3d lh.occip.patch.flat

mris_flatten -w 0 -distances 20 7 rh.occip.patch.3d rh.occip.patch.flat>

And create fieldsign map using-

<fieldsign-sess -a rtopy.self.lh -occip -sf sessid

fieldsign-sess -a rtopy.self.rh -occip -sf sessid>

~Error that analysis isn't retinotopy (because I used -abblocked), retrying step 3 with -retinotopy allowed me to create the fieldsign map.

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For the -abblocked and -retinotopy analysis I am able to look at the results using <tksurfer-sess -a rtopy.self.lh -sf sessid>.

My questions are:

- Should I be using -abblocked or -retinotopy for a polar only design?

- Is it ok to create "faux" eccentricity folders and then only look at the polar data?

- Why is it for either of these analyses I can't view the angle map using <tksurfer-sess -a rtopy.self.?h -s sessid -map angle>? In fact the angle file is not created.

Thanks so much for your time and help.

Daniel

Daniel Cole

University of Rochester

Brain and Cognitive Sciences

dcole10@u.rochester.edu